Epigenomic analysis of formalin-fixed paraffin-embedded samples by CUT&Tag.
Nat Commun
; 14(1): 5930, 2023 09 22.
Article
en En
| MEDLINE
| ID: mdl-37739938
ABSTRACT
For more than a century, formalin-fixed paraffin-embedded (FFPE) sample preparation has been the preferred method for long-term preservation of biological material. However, the use of FFPE samples for epigenomic studies has been difficult because of chromatin damage from long exposure to high concentrations of formaldehyde. Previously, we introduced Cleavage Under Targeted Accessible Chromatin (CUTAC), an antibody-targeted chromatin accessibility mapping protocol based on CUT&Tag. Here we show that simple modifications of our CUTAC protocol either in single tubes or directly on slides produce high-resolution maps of paused RNA Polymerase II at enhancers and promoters using FFPE samples. We find that transcriptional regulatory element differences produced by FFPE-CUTAC distinguish between mouse brain tumors and identify and map regulatory element markers with high confidence and precision, including microRNAs not detectable by RNA-seq. Our simple workflows make possible affordable epigenomic profiling of archived biological samples for biomarker identification, clinical applications and retrospective studies.
Texto completo:
1
Banco de datos:
MEDLINE
Asunto principal:
Cromatina
/
Epigenómica
Tipo de estudio:
Guideline
/
Observational_studies
Límite:
Animals
Idioma:
En
Año:
2023
Tipo del documento:
Article